Edit Molecule Button

/*
* Edit molecule button
*
*
* Usage:
* 1. Edit the name of the Structure field
* 2. Run button script
*
* @author David Pech <[email protected]>
* @author Vita Stejskal <[email protected]>
*/
 
import com.im.df.api.dml.*
import com.im.df.api.*
import com.im.df.api.support.SelectionDescription
import com.im.ijc.core.api.util.IJCCoreUtils
import com.im.ijc.sketchreg.*
import chemaxon.struc.Molecule
import chemaxon.formats.MolExporter
import chemaxon.formats.MolImporter
import com.im.df.api.chem.MarvinStructure
 
init = { widget ->
}
destroy = { widget ->
}
evaluate = { widget ->
def ety = dataTree.rootVertex.entity // assumes you have reference to the data tree
def edp = ety.schema.dataProvider.getEntityDataProvider(ety)
def molFld = ety.fields.items.find { it.name == 'Structure' } // find the structure field
def rs = ety.schema.dataProvider.getDefaultResultSet(dataTree, false, DFEnvironmentRO.DEV_NULL) // find the ResultSet
def rootVS = rs.getVertexState(dataTree.rootVertex) // obtain the VertexState
List ids = rootVS.getSelectedRowsIds() // get the selected IDs
if (ids.size == 1) {
Map rows = rootVS.getData(ids, DFEnvironmentRO.DEV_NULL) // get the data
Map row = rows[ids[0]] // get the first and only row
MarvinStructure mol = row[molFld.id] // Get the Structure. Its a com.im.df.api.chem.MarvinStructure instance
Molecule cxnMol = mol.getNative() // obtain the chemaxon.struc.Molecule instance
// convert chemaxon.struc.Molecule instance into canonical SMILES
molSmiles = cxnMol.toFormat("smiles:u")
// using SketchRegistry uses the default Sketcher
// so this will work with both Marvin or ChemDraw
SketchRegistry registry = SketchRegistry.getDefault()
Sketch sketcher = registry.getDefaultFactory().createSketcher()
sketcher.setDialogTitle('My Molecule sketcher')
// load current molecule into the Sketcher
sketcher.setMolecule(MolImporter.importMol(molSmiles))
sketcher.setSketchFeedback(new SketchFeedback() {
public boolean buttonPressed(Sketch sketch, String buttonName) {
println 'Button pressed: ' + buttonName
// do something when button in Sketcher is pressed
}
public void moleculeChanged(Sketch sketch) {
//println 'Sketcher: ' + MolExporter.exportToFormat(sketch.getMolecule(), 'smiles')
// rewrite structure in the database with the changed one
def dataToUpdate = [(molFld.id):MolExporter.exportToFormat(sketch.getMolecule(), 'smiles')]
def lock = edp.lockable.withLock('Updating') { envRW ->
def ud = DFUpdateDescription.create(ety, ids[0], dataToUpdate)
def submitList = Collections.singletonList(ud)
edp.update(submitList, DFUndoConfig.OFF, envRW)
}
println "Molecule edited"
}
})
sketcher.openSketcher()
} else {
println "Bad Selection"
}
}
on_change = { widget, button ->
}